That would probably be a good thing. I have tried countering large amounts of bombers with large amounts of fighters, but it wasn't that effective (last time I tried it a long time ago...).
What if fighters/bombers had some special abilities/weapons that were limited in shots and couldn't be refreshed till they landed and reloaded?
While I REALLY want strikecraft to be allowed to have active abilities for modding reasons, I don' think that is a good idea for balance purposes. Strikecraft do not last long and are regenerated for free, and each time a strikecraft is rebuilt is can then immediately use that ability/weapon.
I also think it falls under the "It makes the game more complicated than it adds to strategic depth". Sins is at hard a more strategic game, and having to worry about ammo and fuel for example are really more suited for tactical simulations.